Supermolecule Model Research Articles

Optical and structural properties of an octupolar salt: Triphenylguanidinium trithiocyanurate

A new triphenylguanidinium salt, triphenylguanidinium trithiocyanurate, has been synthesized and characterized by single-crystal X-ray diffraction revealing a monoclinic centrosymmetric assembling of cations and anions. The crystal structure of title salt contains ribbons propagating along the b axis, assembled by two strong N–H⋯S hydrogen bonds between the neighboring negative ions. The trithiocyanurate ion exhibits a characteristic fingerprint plot, that has been found in similar salts. Hyperpolarizabilities of anions, cations and their neutral cluster were calculated using Density Functional Theory and the functional CAM-B3LYP. Using a combined approach between the supermolecule model and oriented gas model, the predicted third harmonic generation is 40 times that of fused silica.

Solvent effect on static and dynamic first hyperpolarizability of azochromophore with tricyanopyrrole acceptor moiety

Solvent effect on molecular nonlinear optical (NLO) characteristics of azochromophore with tricyanopyrrole acceptor, AAB-TCP, is estimated within different models: polarizable continuum model (PCM), supermolecule (SM), semicontinuum (SC). The values of first hyperpolarizability are calculated by TD-DFT at M06-2X/aug-cc-pVDZ level; the dynamic characteristics are evaluated at 0.65 eV frequency. Molecular dynamics of AAB-TCP solution in acetone (at concentration 2·10−2 mol%) is performed in amorphous cell what allowed to reveal different types of hydrogen-bonded supermolecules formed by AAB-TCP and one or two acetone molecules; for four supermolecules the first hyperpolarizability values are calculated. Solvent effect accounted within the PCM approach causes almost 4 times increase of static first hyperpolarizability. The account of direct interaction within supermolecule model results in the growth of first hyperpolarizability and describes the solvent effect partly; the estimations at semicontinuum level show further increase (by 40% for static and 50% for dynamic cases) of first hyperpolarizability compared to the PCM values, thus demonstrating the role of solute-solvent hydrogen bonding.

Alternative Non-Ionic Pathway for Uncatalyzed Prins Cyclization: DFT Approach

Density functional theory calculations (ωB97X-D/6-311++G(d,p)) are employed to investigate an alternative pathway for Prins-like cyclization. Although strong acids usually catalyze this reaction, 4-amino-1,3-dioxanes are rapidly obtained in high yields without catalyst when benzenamines and acetaldehyde react at low temperatures, in aqueous medium. Considering these conditions, we applied a supermolecule model with explicit water molecules to compute the mechanism for 4-amino-1,3-dioxanes formation from the reactants. The structure of the primary solvation shell was determined by Metropolis Monte Carlo method. In the Prins-cyclization step, we found an unpredicted pathway with non-ionic transition structures or intermediates. Explicit water molecules establish a net of hydrogen bonds allowing prototropism, maintaining the electrical neutrality in the system while two protons transfer occurs. To provide data to further experimental confirmation of this hypothesis, we estimated the kinetic isotope effect for the reaction. We also investigated the use of aliphatic amines, which indicates that the reaction may be of a broader application than first observed experimentally.

Tautomerization, acidity, basicity, and stability of cyanoform: a computational study.

BackgroundCyanoform is long known as one of the strongest acid. Cyanoform is only stable below −40 °C. The issue of the stability and tautomeric equilibria of cyanoform (CF) are investigated at the DFT and MP2 levels of theory. The present work presents a detailed study of structural tautomer interconversion in three different media, namely, in the gas phase, in a solvent continuum, and in a microhydrated environment where the first solvation layer is described explicitly by one or two water molecule. In all cases, the transition state has been localized and identified. Proton affinities, deprotonation energies and the Raman spectra are reported analyzed and discussed.ResultsThe 1 tautomer of cyanoform is shown to be more stable than 2 form by only 1.8 and 14.1 kcal/mol in the gas phase using B3LYP/6-311 ++G** and MP2/6-311 ++G** level of theory, respectively. This energy difference is reduced to 0.7 and 13.4 kcal/mol in water as a solvent using CPCM model using B3LYP/6-311 ++G** and MP2/6-311 ++G** level of theory, respectively. The potential energy barrier for this proton transfer process in the gas phase is 77.5 kcal/mol at MP2/6-311 ++G** level of theory. NBO analysis, analysis of the electrostatic potential (ESP) of the charge distribution, donor–acceptor interactions and charge transfer interactions in 1 and 2 are performed and discussed.ConclusionsGross solvent continuum effects have but negligible effect on this barrier. Inclusion of one and two water molecules to describe explicitly the first solvation layer, within the supermolecule model, lowers the barrier considerably (29.0 and 7.6 kcal/mol, respectively). Natural bond orbital (NBO) analysis indicated that the stability of the cyanoform arising from charge delocalization. A very good agreement between experimental and theoretical data has been found at MP2/6-311 ++G** for the energies. On other hand, B3LYP/6-311 ++G** level of theory has good agreement with experimental spectra for CF compound.Electronic supplementary materialThe online version of this article (doi:10.1186/s13065-016-0166-z) contains supplementary material, which is available to authorized users.

Theoretical investigation of the thermodynamic structures and kinetic water-exchange reactions of aqueous Al(III)–salicylate complexes

Density functional theory (DFT) calculations were performed on the structures and water-exchange reactions of aqueous Al(III)–salicylate complexes. Based on the four models (gas phase (GP); polarizable continuum model (PCM), which estimates the bulk solvent effect; supermolecule model (SM), which considers the explicit solvent effect, and supermolecule–polarizable continuum model (SM–PCM), which accounts for both types of solvent effects), we systematically conducted this study by examining three different properties of the complexes. (1) The microscopic properties of the aqueous Al(III)–salicylate complexes were studied by optimizing their various structures (including the possible 1:1 mono- and bidentate complexes, cis and trans isomers of the 1:2 bidentate complexes and 1:3 bidentate complexes) at the B3LYP/6-311+G(d, p) level. (2) The 27Al and 13C NMR chemical shifts were calculated using the GIAO method at the HF/6-311+G(d, p) level. The calculation results show that the values obtained with the SM–PCM models are in good agreement with the experimental data available in the literature, indicating that the models we employed are appropriate for Al(III)–salicylate complexes. (3) The water-exchange reactions of 1:1 mono- and bidentate Al(III)–salicylate complexes were simulated using supermolecule models at the B3LYP/6-311+G(d, p) level. The logarithm of the water-exchange rate constant (logkex) of the 1:1 bidentate complex predicted using the “logkex–dAl–OH2” correlation is 4.0, which is in good agreement with the experimental value of 3.7, whereas the calculated range of logkex of the 1:1 monodentate complexes is 1.3–1.9. By effectively combining the results for the thermodynamic static structures with the simulations of the kinetic water-exchange reactions, this work promotes further understanding of the configurations and formation mechanism of Al(III)–salicylate complexes.

Are the Intramolecular O–H···F and O–H···Cl Hydrogen Bonds Maintained in Solution? A Theoretical Study

The present case study aims at calculating the equilibrium conformer compositions for 2X-ethanol and 2X-phenol (X = F, Cl) in solution, and exploring the effect of the applied theoretical method and basis set on the obtained results, as well as considering the usefulness of the continuum solvent approach in comparison with the explicit solvent Monte Carlo model utilizing the free energy perturbation method. Gas-phase optimizations at the DFT/B97D/aug-cc-pvtz and ab initio MP2/aug-cc-pvtz levels predicted structures in good agreement with the available experimental data for three test molecules. Because in-solution geometries change only slightly according to the IEF-PCM continuum solvent calculations in carbon tetrachloride and water, the two theoretical levels were applied further on, and complete basis set (CBS) relative internal free energies were estimated for the conformers under study. The predicted OCCF gauche/trans ratio for 2F-ethanol was well reproduced in comparison with available experimental compositions. The predominant gauche structure maintains an intramolecular hydrogen bond in carbon tetrachloride (HB structure), whereas HB and NoHB gauche conformers appear in nearly the same fraction in aqueous solution. The internally hydrogen-bonded conformer is predominant also for 2X-phenol species, as calculated on the basis of relative CBS internal free energies and IEF-PCM and FEP/MC solvation free energies. Use of a trihydrate supermolecule model for 2F-ethanol conformers leads to the prediction of the aqueous-solution composition in contrast to the experiment. Solution structure modeling predicts weak hydrogen-bond formation capacity for both the covalently bound F and Cl atoms, even in conformations where they are fully exposed to hydration.

Alkaline hydrolysis of ethylene phosphate: An ab initio study by supermolecule model and polarizable continuum approach

The alkaline hydrolysis reaction of ethylene phosphate (EP) has been investigated using a supermolecule model, in which several explicit water molecules are included. The structures and single-point energies for all of the stationary points are calculated in the gas phase and in solution at the B3LYP/6-31++G(df,p) and MP2/6-311++G(df,2p) levels. The effect of water bulk solvent is introduced by the polarizable continuum model (PCM). Water attack and hydroxide attack pathways are taken into account for the alkaline hydrolysis of EP. An associative mechanism is observed for both of the two pathways with a kinetically insignificant intermediate. The water attack pathway involves a water molecule attacking and a proton transfer from the attacking water to the hydroxide in the first step, followed by an endocyclic bond cleavage to the leaving group. While in the first step of the hydroxide attack pathway the nucleophile is the hydroxide anion. The calculated barriers in aqueous solution for the water attack and hydroxide attack pathways are all about 22 kcal/mol. The excellent agreement between the calculated and observed values demonstrates that both of the two pathways are possible for the alkaline hydrolysis of EP.

DFT studies of Al–O Raman vibrational frequencies for aquated aluminium species

Raman frequency calculations of Al ( H 2 O ) 6 3 + and Al ( OH ) 4 - species in different models were carried out with density functional theory (DFT). Gas-phase model (GP), polarizable continuum model (PCM), supermolecule model (SM) and supermolecule-polarizable continuum model (SM-PCM) were considered and frequencies over the wavenumber range from 0 to 1000 cm −1 were discussed. The calculated frequencies of the two species in SM-PCM model are in fair agreement with the observed frequencies in aqueous solution and the average deviation is 6 cm −1. Based on the results of Al ( H 2 O ) 6 3 + and Al ( OH ) 4 - , the DFT method and the SM-PCM model were used to study the Al–O Raman bands for some other monomeric and dimeric aluminiums. The monomeric aluminiums Al(OH) 2+, Al ( OH ) 2 + and Al ( OH ) 6 3 - as well as the dimer Al 2 O ( OH ) 6 2 - were included. As a result, we predict the main Al–O skeleton vibrations of Al ( OH ) ( H 2 O ) 5 2 + at 685 cm −1, trans- Al ( OH ) 2 ( H 2 O ) 4 + at 542 cm −1, Al ( OH ) 6 3 - at 510 cm −1 and Al 2 O ( OH ) 6 2 - at 510 and 699 cm −1 respectively in Raman spectra of aqueous solution. It can also be concluded that the calculated frequencies of Al 2 O ( OH ) 6 2 - are close to the experimental values and the existence of Al ( OH ) 6 3 - in aluminate solution cannot be ruled out.

Density functional theory study and kinetic analysis of the formation mechanism of Al30O8(OH)56(H2O)2618+ (Al30) in aqueous solution

Abstract The formation mechanism of Al 30 O 8 (OH) 56 (H 2 O) 26 18+ (Al 30 ) has been investigated by the density functional theory based on the supermolecule model and kinetic analysis on the 27 Al nuclear magnetic resonance (NMR) experimental results in monitoring Al 30 synthesis process. The theoretical chemistry calculations on the four possible schemes show that δ-Na–Al 13 is the reasonable intermediate followed by the substitution of Na with Al to form δ-Al 14 , and Na + plays an important role in stabilizing the intermediate (δ-Na–Al 13 ) in the transformation. The kinetic analysis on the 27 Al NMR experimental data indicates that e-Al 13 decomposes and isomerizes in the formation of Al 30 , while Al monomers facilitate the decomposition of e-Al 13 and so the isomerization of e-isomers to δ-isomers effectively. The favorable formation mechanism of Al 30 includes three steps: (1) e-Al 13 decomposes and rearranges into the isomer δ-Al 13 ; (2) Na + reacts with δ-Al 13 to stabilize the intermediate δ-Na–Al 13 , followed by Al monomers replacing Na to form δ-Al 14 ; (3) δ-Al 14 reacts with the Al monomers in the solution to finally form Al 30 . Both Al monomers and Na + are important in the transformation. Al monomers are the basic building units and helpful to the isomerization while Na + can well stabilize the isomer δ-Al 13 to yield intermediate δ-Na–Al 13 . The results also show that other isomers of e-Al 13 (β-Al 13 and α-Al 13 ) form in the formation of Al 30 , and their calculated 27 Al NMR tetrahedral resonance shifts are consistent with the experimental 27 Al NMR tetrahedral signals in the preparation process of Al 30 .

In silico approach to cisplatin toxicity. Quantum chemical studies on platinum(II)–cysteine systems

The behaviour of cisplatin in serum, and the drastic differences between the properties of this drug and its trans-isomer were the main motivations for this work. In a search for model "thiol-platin(II)" interactions, the first steps of the following reaction systems were evaluated: (1) cisplatin-thiomethanol; (2) transplatin-thiomethanol; (3) cisplatin-cysteine; and (4) transplatin-cysteine. In each case, calculations for the associative mode of reactions were performed. The electronic structure of these molecular systems was studied at the non-empirical all-electron level using density functional theory (DFT) within the Huzinaga and WTBS basis sets including polarisation Gaussian functions and full geometry optimisation. B3LYP or EPBO density functionals were applied throughout. The calculated molecular electrostatic potentials are presented graphically. Assuming that electrostatic effects are dominant, cisplatin should interact more strongly with the sulfur atom of CH3S- and deprotonated CYS-S- than transplatin. This fact has been documented in the supermolecule model of the relevant interaction energies in both gas phase as well as within the solvent polarisable continuum model. The opposite relationship was observed when we compared values of energy differences between products and substrates for both isomers. The data obtained here could be applied to search for correlation between the biological activity of platinum complexes and their properties as estimated by various physico-chemical and in silico methodologies.

Theoretical investigation of dehydration of aquated Al(OH)2+ species in aqueous solution

Reaction pathways, solvent effects and energy barriers have been investigated for the dehydration processes of aquated Al(OH)(2)(+) species in aqueous solution by density functional calculations using a supermolecule model. The dehydration processes from Al(H(2)O)(4)(OH)(2)(+) to Al(H(2)O)(2)(OH)(2)(+) involve the water exchange on cis-Al(H(2)O)(4)(OH)(2)(+) and dehydration of the following intermediate pentacoordinate Al(H(2)O)(3)(OH)(2)(+). The calculated results indicate that cis-Al(H(2)O)(4)(OH)(2)(+) exchanges water in a dissociative way with an activation energy of 27.7 kJ mol(-1). Loss of coordinated water from hexacoordinate and pentacoordinate Al(OH)(2)(+) is unfavourable by 22.1 and 6.6 kJ mol(-1), respectively, which supports the presence of the stable hexacoordinate Al(H(2)O)(4)(OH)(2)(+) in aqueous solution. Our results also indicate that both the explicit water molecules and bulk water molecules have great influences on the energy barriers, and they can not be neglected.

NaSCN: Striking Differences Between Its Gas‐Phase and Crystal‐Phase Structure: A Theoretical Study

AbstractFor Abstract see ChemInform Abstract in Full Text.

Solids modeled by ab initio crystal field methods, part 22: the Fock matrix transformed supermolecule model and the structure determination of D-erythronic acid-3,4-carbonate.

To eliminate the cutoff effects in the supermolecule model (SM), the Fock matrix transformed supermolecule model (FTSM) is developed. In this model a cyclization of the cluster is performed by means of transformations of elements of the Fock matrix, thereby restoring the translational symmetry. Besides this fundamental enhancement, significant CPU time savings are realized because, in this new procedure, not all Fock matrix elements need to be calculated. The method is applied in a study of the structure of D-erythronic acid-3,4-carbonate in the crystal phase, where the new model is compared to the supermolecule model as well as the XRD experiment. The results are found to be in good agreement with experimental data.

NaSCN: Striking Differences between Its Gas-Phase and Crystal-Phase Structure: A Theoretical Study

A detailed investigation of the gas-phase and crystal-phase structure of sodium thiocyanate has been presented. Using highly sophisticated ab initio calculations (MP2, QCISD, CCSD(T), CBS-Q), the existence of the four-membered ring monomer has been predicted. Three minima have been found on the PES of the NaSCN dimers using HF, B3LYP, and MP2 methods, and two of these have been identified as the main building blocks of the NaSCN crystal. The systematic enlargement of the clusters along the crystal axes at the HF level led to the convergence of the geometrical parameters and the interaction energy of the clusters. According to our results, the supermolecule model with one layer of molecules around the central molecule is not large enough to simulate the overall crystal structure of NaSCN, but the supermolecule model with a 17-member supermolecule (two layers of neighbors) has been successfully applied and found to be in excellent agreement with the experimental data, the principal findings, and point out major conclusions.

First-principles studies of C-13 NMR chemical shift tensors of amino acids in crystal state

A series of gauge-independent atomic orbital (GIAO) magnetic shielding calculations with ab initio Hartree–Fock (HF) and density-functional theory (DFT) methods were performed on alanine, asparagine, aspartic acid, cysteine, glutamine, glycine, histidine, serine, and tyrosine in crystal state to study their 13C NMR chemical shift tensors. The GIAO calculations on the amino acids were performed with and without inclusion of the crystal environment. Compared to previous computational studies reported in literature, this study accounts for more complete crystal environmental effects on the 13C NMR chemical shifts and, therefore, provides calculated results in better agreement with the experimental data. For each amino acid considered, the crystal environment included in the calculations includes all molecules having hydrogen bonds with the target molecule. It has been shown that the 13C NMR chemical shift tensors, particularly the principal components δ 11 and δ 22, calculated without inclusion of the crystal environment significantly differ from the corresponding experimental data for the carbon atoms that are close to a hydrogen bond in the crystal, although the calculated isotropic 13C chemical shifts are in good agreement with the experimental data. The GIAO calculations including the crystal environment with both the HF and DFT methods can significantly improve the calculated 13C chemical shift tensors. The results calculated with the DFT method are slightly better than the corresponding results with the HF method. The good agreement between the calculated and experimental results indicate that the significant crystal environmental effects on the principal components of 13C chemical shift tensors of the amino acids are mainly attributed to the hydrogen bonding of amino acid with its environment. When all the hydrogen bonds of amino acid with its environment are included explicitly in the GIAO calculation with a supermolecule model, the calculated 13C chemical shift tensors are in good agreement with the corresponding experimental data. This insight obtained from studying the crystal environmental effects on 13C chemical shift tensors of amino acids in crystal state could also be useful for future computational studies of the protein environmental effects on 13C chemical shift tensors of amino acid residues of proteins.

Ab initio investigation of the Young's modulus of polyamide‐6

AbstractThe Young's modulus of the α form of polyamide‐6 has been calculated using the supermolecule model. The crystalline polymer was represented by a single‐chain molecule, divided into a head, body, and tail part. The body of the model contains an even number of polyamide‐6 units (4–16 units) and is representative for a polyamide‐6 chain. The periodicity of the system was not explicitly taken into account, but in a few tests the effect of a linear constraint has been evaluated. An n‐butyl and n‐pentyl group have been used as head and tail, respectively. In a number of additional calculations the length of the head and tail has been varied. For all supermolecule models the equilibrium and elongated structures have been optimized using ab initio Hartree–Fock calculations with a 6‐31G** basis set. From the energy values of the optimized structure a Young's modulus of 334 GPa has been extrapolated for both the unconstrained and linearly constrained models. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003

A Linearly Scaling QM/MM Method to Study Molecular Crystals Using BRABO/CHARMM: Application to 2-(2-Methyl-3-chloroanilino) Nicotinic Acid

Molecular crystals have been studied using two new forms of the cluster approach: an extended point charge (PCX) and an extended supermolecule (SMX) model. These models extend, using a hybrid quantum mechanical/ molecularmechanical (QM/MM) approach, that part of the molecular environment that was previously described by point charges in, respectively, the point charge (PC) and supermolecule (SM) models. After interfacing the ab initio program BRABO with the molecular mechanics program CHARMM, the PCX and SMX models have been tested on formamide oxime, α-glycine, and the yellow form of dimethyl 3,6-dichloro-2,5-dihydroxyterephthalate. PCX results are in notably better agreement with experimental results than PC results and are shown to be a viable alternative to SM calculations. For α-glycine, the SMX model improves results over the SM model. For dimethyl 3,6-dichloro-2,5-dihydroxyterephthalate, it was shown that the SMX model can give SM-quality results when fewer neighbors are included in the wave function, thereby reducing the computation time significantly. As a second part of this study, the PCX model was applied to the geometry optimization of the four polymorphs of 2-(2-methyl-3-chloroanilino) nicotinic acid. In contrast to a previous study using the PC model, the newly developed PCX model introduced in this study allowed full geometry optimization of all polymorphs.

Ab initio calculation of the Young's modulus of α‐polyamides

AbstractIn earlier works the supermolecule model has been applied to the calculation of the Young's modulus of crystalline polyethylene and polyamide‐6. In the supermolecule model a crystalline polymer is represented as a single finite chain divided into a head, body, and tail part. The body contains a number of monomer units and is representative for a polymer chain. In this article, this model has been used to study the geometric properties and the elastic moduli of the α form of other polyamides: polyamide‐2 (or polyglycine), polyamide‐3, polyamide‐4, polyamide‐11, and polyamide‐6,6. All calculations have been performed with a linearly constrained body. The results have been compared to other theoretical and experimental results if available. © 2002 Wiley Periodicals, Inc.; DOI 10.1002/qua.2002;10121

MC/MO Study of the Solvent Effect on the Excitation Energies of the (CH3)2NO Radical in Hydrogen-Bonding and Non-Hydrogen-Bonding Solvents

A combination of Monte Carlo (MC) simulation and ab initio molecular orbital (MO) calculation was applied to dimethyl nitroxide (DMNO) in H2O, CH3OH, CH3CN, and (CH3)2CO solutions, and the solvent effect on the electronic structure and n−π* and π−π* excitation energies was analyzed. The solution structures were generated by MC simulations, and the ROHF-SCI calculation with the MIDI-4 basis set was carried out for each solution structure. The electronic structure and excitation energies in the four solutions were obtained by averaging the 100 solution structures for each solution. Solvent effect was calculated by the point charge model and supermolecule model. In the point charge model, all solvent molecules were approximated by point charges at atomic nuclei, while in the supermolecule model the solute molecule and some of the solvent molecules were treated as a supermolecule surrounded by other solvent molecules approximated by point charges. The calculated n−π* excitation energy increased (blue shift) in the four solvents as compared to that in the gas phase. The magnitude of the solvent effect reflects the dielectric constant of the solvent. The calculated En-π* value in CH3OH was larger than that in CH3CN, whose dielectric constant is larger than that of CH3OH. This is due to the hydrogen-bonding ability of CH3OH and agrees well with experiment. The π−π* excitation energy was predicted to decrease in the four solvents, although the red shift was overestimated. The solvent effect was well elucidated by using the Mulliken charges of DMNO in the ground state and the excited states and the electrostatic potential generated by the solvent molecules.

Solids modeled by ab initio crystal field methods. Part 19. Structure of yellow and light yellow form of dimethyl 3,6-dichloro-2,5-dihydroxyterephthalate

Dimethyl 3,6-dichloro-2,5-dihydroxyterephthalate is known for its color polymorphism in the solid state. For the yellow and light yellow form of this compound the geometry has been optimized using a supermolecule (SM) model. A cluster including the central molecule and the 14 nearest neighboring molecules was described by an ab initio Hartree–Fock wave function. This cluster was surrounded by other molecules represented by point charges placed at the atomic positions. The radius of the complete model was approximately 20 Å. The geometry of dimethyl 3,6-dichloro-2,5-dihydroxyterephthalate in the solid state has been compared to the optimized geometry of an isolated molecule in order to identify the crystal field effects. The structural differences between both polymorphic forms are well described using the SM model. The influence of the intermolecular interactions on the electron distribution of the individual molecules has been studied using the cluster deformation electron density distribution.